ATP9A

Chr 20q13.2

ATPase phospholipid transporting 9A

Aliases:: KIAA0611, ATPIIA
MANE:: ENST00000338821.6

OMIM: 609126 ↗NCBI: 10079 ↗Ensembl ↗

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Predicted protein structure

AlphaFold predicted structure

ATP9A · O75110

v62025-08-01

Predicted Aligned Error matrix for ATP9A — diagonal shows residue index, colour shows pairwise prediction confidence (lower is better) — Predicted Aligned Error

Mean pLDDT

84.2/ 100

Confident

1,047 residues

Confidence breakdown

Very high(≥ 90)41%
Confident(70–90)50%
Low(50–70)3%
Very low(< 50)6%

Open interactive 3D viewer

AlphaFold (Jumper et al., 2021) · CC BY 4.0

Clinical relevance (Genomics England PanelApp)

Diagnostic Grade (Green)

DDG2P
BIALLELIC, autosomal or pseudoautosomal
Intellectual disability
BIALLELIC, autosomal or pseudoautosomal
Severe microcephaly
BIALLELIC, autosomal or pseudoautosomal

Disease associations (Open Targets)

neurodevelopmental disorder with poor growth and behavioral abnormalities
0.71
Failure to thrive
0.42
Secondary microcephaly
0.42
Abnormality of the skeletal system
0.41
Intellectual disability
0.37
Global developmental delay
0.37
complex neurodevelopmental disorder
0.37
Abnormal abdomen morphology
0.37
osteoarthritis, knee
0.35
alcohol drinking
0.34

Score is the Open Targets composite evidence score (0-1). Higher = stronger gene-disease association.

Protein function (UniProt)

Probable phospholipid-transporting ATPase IIA

Plays a role in regulating membrane trafficking of cargo proteins, namely endosome to plasma membrane recycling, probably acting through RAB5 and RAB11 activation (PubMed:27733620, PubMed:30213940, PubMed:36604604). Also involved in endosome to trans-Golgi network retrograde transport (PubMed:27733620, PubMed:30213940). In complex with MON2 and DOP1B, regulates SNX3 retromer-mediated endosomal sorting of WLS, a transporter of Wnt morphogens in developing tissues. Participates in the formation of endosomal carriers that direct WLS trafficking back to Golgi, away from lysosomal degradation (PubMed:30213940). Appears to be implicated in intercellular communication by negatively regulating the release of exosomes (PubMed:30947313). The flippase activity towards membrane lipids and its role in membrane asymmetry remains to be proved (PubMed:30947313). Required for the maintenance of neurite morphology and synaptic transmission (By similarity)